Disclaimer: I have never done a transom job, nor have I paid anyone to do it, these comments are merely my opinion based on what I know about boats in general, and SeaCrafts specifically.
Best design/modification - this is up for debate, but I'm sure most members will agree that enclosing a 23's transom and adding a floatation bracket is the way to go. I personally prefer the aesthetics of a notched transom, but it's hard to argue the benefits of enclosing/bracketing. Another modification would be running the scuppers out through the transome versus through the hull bottom.
Compromises - I don't know about SCs specifically, but I've been in other bracketed boats (single OB) that have a tough time in reverse. Control in tight spaces is an issue. With a notched transom, raising the height does not compromise any handling/performance characteristics provided the OB is mounted properly.
Original design a must change? - Besides the original scupper design, another of the 23's Achilles heels is the splashwell design. In a lot of instances, raw water can run into the bilge while backing down or taking a wave over the back. Do you NEED to change it? Not necessarily, but if you're redoing the transom, now is the time to make the necessary modifications to improve the design.